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Open data
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Basic information
Entry | Database: PDB / ID: 3o1b | ||||||
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Title | CRYSTAL STRUCTURE OF DIMERIC KLHXK1 IN CRYSTAL FORM II | ||||||
![]() | Hexokinase | ||||||
![]() | TRANSFERASE / RNaseH-like fold / Hexokinase / Glycolysis / Glucose repression / ATP binding / Mig1 binding | ||||||
Function / homology | ![]() mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / mannose metabolic process / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion ...mannokinase activity / hexokinase / fructokinase activity / glucokinase activity / mannose metabolic process / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kuettner, E.B. / Kettner, K. / Keim, A. / Kriegel, T.M. / Strater, N. | ||||||
![]() | ![]() Title: Crystal Structure of Hexokinase KlHxk1 of Kluyveromyces lactis: A MOLECULAR BASIS FOR UNDERSTANDING THE CONTROL OF YEAST HEXOKINASE FUNCTIONS VIA COVALENT MODIFICATION AND OLIGOMERIZATION. Authors: Kuettner, E.B. / Kettner, K. / Keim, A. / Svergun, D.I. / Volke, D. / Singer, D. / Hoffmann, R. / Muller, E.C. / Otto, A. / Kriegel, T.M. / Strater, N. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization and preliminary X-ray diffraction studies of hexokinase KlHxk1 from Kluyveromyces lactis Authors: Kuettner, E.B. / Kriegel, T.M. / Keim, A. / Naumann, M. / Strater, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.6 KB | Display | ![]() |
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PDB format | ![]() | 159.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.1 KB | Display | ![]() |
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Full document | ![]() | 426.6 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3o08SC ![]() 3o1wC ![]() 3o4wC ![]() 3o5bC ![]() 3o6wC ![]() 3o80C ![]() 3o8mC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53672.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.07 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1microL reservoir + 1microL protein; reservoir: 22% PEG6000, 0.1M Tris pH 8.0, protein: 10mg/ml KlHxk1, 10mM Tris pH 7.4, 1mM EDTA, 1mM DTT, 0.5mM PMSF , VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 28, 2004 |
Radiation | Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 11502 / % possible obs: 82.7 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 49.1 Å2 / Rsym value: 0.067 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 858 / Rsym value: 0.171 / % possible all: 62.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3O08 Resolution: 2.8→29.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 33.812 / SU ML: 0.29 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FULL B FACTORS AND ANISO RECORDS WERE COMPUTED BY CCP4 PROGRAMM TLSANL.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.091 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→29.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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